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From: William P. <wil...@ya...> - 2010-03-24 02:43:56
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On Mar 23, 2010, at 9:41 PM, Rutger Vos wrote: > In theory it should be possible to delete a matrix from the matrixList > page, but in practice clearing out all the matrix elements takes so > long it hampers userfriendliness, no? Currently deleting even small matrices cause a proxy time-out. We're working of fixing this. The other thing that was never implemented in the original code is that taxon labels belonging to a deleted matrix or tree do not get deleted themselves, even if they are not used by anything else. Hence garbage builds up -- and it's confusing to the submitter to still find taxon labels there after deleting all matrices and trees. So we're also working to fix this. Youjun will try to implement this in the usual java-hibernate way, but if that proves too slow, other solutions like a Postgresql stored procedure might need to be used. bp |
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From: Hilmar L. <hl...@ne...> - 2010-03-24 02:01:16
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On Mar 23, 2010, at 9:30 PM, William Piel wrote: > By the way, how do I get access to the help ticketing system? Go to https://help.nescent.org/ . Your username is wil...@ya.... There should be a button to have the system send you a new password if you don't know it anymore. You should have full permissions to the treebase-bugs and treebase- help queue. Who will be triaging the bugs so that those that are real and can't be addressed immediately get transferred to the Sf.net tracker? Let me know if that's Youjun and I'll add him to the queue watchers. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-03-24 01:41:43
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In theory it should be possible to delete a matrix from the matrixList page, but in practice clearing out all the matrix elements takes so long it hampers userfriendliness, no? On Wednesday, March 24, 2010, Vladimir Gapeyev <vla...@du...> wrote: > It's only possible to delete the whole submission, not its individual parts, right? --VG > > Begin forwarded message: > From: "Elizabeth H. Zacharias via RT" <he...@tr...>Date: March 23, 2010 7:26:29 PM EDTTo: undisclosed-recipients: ;Subject: [[treebase-help] #7630] TreeBASE Submission S10318Reply-To: he...@tr... > > Tue Mar 23 19:26:28 2010: Request 7630 was acted upon. > Transaction: Ticket created by eza...@oe... > Queue: Treebase-help > Subject: TreeBASE Submission S10318 > Owner: Nobody > Requestors: eza...@oe... > Status: new > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7630 > > > > Hello, > I am trying to delete my matrix to upload the corrected one but I > can't seem to delete it. Would you help me? > Thank you, > Elizabeth Zacharias > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Elizabeth H. Zacharias, Ph.D. > Harvard University Herbaria | 22 Divinity Avenue | Cambridge, MA > 02138 | U.S.A. > Tel. 1-617-496-8514 (direct) | Fax. 1-617-495-9484 | www.huh.harvard.edu > > > > > > > > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-24 01:37:34
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Youjun is working on solving the deleting-matrix problem. I don't think that deleting submissions work either. I'm suggesting to her that she rename her matrices "don't use" and simply not include them in any analysis. By the way, how do I get access to the help ticketing system? bp On Mar 23, 2010, at 9:17 PM, Vladimir Gapeyev wrote: > It's only possible to delete the whole submission, not its individual parts, right? > --VG > > Begin forwarded message: > >> From: "Elizabeth H. Zacharias via RT" <he...@tr...> >> Date: March 23, 2010 7:26:29 PM EDT >> To: undisclosed-recipients: ; >> Subject: [[treebase-help] #7630] TreeBASE Submission S10318 >> Reply-To: he...@tr... >> >> >> Tue Mar 23 19:26:28 2010: Request 7630 was acted upon. >> Transaction: Ticket created by eza...@oe... >> Queue: Treebase-help >> Subject: TreeBASE Submission S10318 >> Owner: Nobody >> Requestors: eza...@oe... >> Status: new >> Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7630 > >> >> >> Hello, >> I am trying to delete my matrix to upload the corrected one but I >> can't seem to delete it. Would you help me? >> Thank you, >> Elizabeth Zacharias >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Elizabeth H. Zacharias, Ph.D. >> Harvard University Herbaria | 22 Divinity Avenue | Cambridge, MA >> 02138 | U.S.A. >> Tel. 1-617-496-8514 (direct) | Fax. 1-617-495-9484 | www.huh.harvard.edu >> |
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From: Vladimir G. <vla...@du...> - 2010-03-24 01:18:00
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It's only possible to delete the whole submission, not its individual parts, right? --VG Begin forwarded message: > From: "Elizabeth H. Zacharias via RT" <he...@tr...> > Date: March 23, 2010 7:26:29 PM EDT > To: undisclosed-recipients: ; > Subject: [[treebase-help] #7630] TreeBASE Submission S10318 > Reply-To: he...@tr... > > > Tue Mar 23 19:26:28 2010: Request 7630 was acted upon. > Transaction: Ticket created by eza...@oe... > Queue: Treebase-help > Subject: TreeBASE Submission S10318 > Owner: Nobody > Requestors: eza...@oe... > Status: new > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7630 > > > > Hello, > I am trying to delete my matrix to upload the corrected one but I > can't seem to delete it. Would you help me? > Thank you, > Elizabeth Zacharias > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Elizabeth H. Zacharias, Ph.D. > Harvard University Herbaria | 22 Divinity Avenue | Cambridge, MA > 02138 | U.S.A. > Tel. 1-617-496-8514 (direct) | Fax. 1-617-495-9484 | www.huh.harvard.edu > > > > > > > > > |
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From: Rutger V. <rut...@gm...> - 2010-03-23 07:46:46
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Ok, I'll spend more time on this this evening. On Tuesday, March 23, 2010, William Piel <wil...@ya...> wrote: > > On Mar 22, 2010, at 7:13 PM, Rutger Vos wrote: > I did some checking and fixing to make the static pages all xhtml > compliant. Can we all do that right away when we create html in the > jsps? I know we all pretty much know the rules, but the number of > validation errors in the recently created pages was horrendous :-) > > I fixed the analysis page such that it functions and looks the way > it's supposed to in IE8, but I have no way to check IE7. > > I also added the functionality where all but the last analysis is > collapsed by default. > > Thanks for the fix. > I found a Parallels VM with IE6 on it, so I was able to test that. Then I downloaded IE7 and tested that. IE8 wouldn't install, so I used an emulator (http://www.my-debugbar.com/wiki/IETester/HomePage). > Here are the damages: > * None of the IE versions can work with our analysis entry forms (the current build -- not yours, obviously) > * IE6 and IE7 throw exceptions for almost all of our search buttons (the barf below is from entering a name and clicking the "Author" button -- I guess it's passing 'Study ID' instead of 'authorKeyword' button -- or something like that). > * IE8 works on most buttons but fails on the "Discard All Results" buttons (on all tabs) > Since IE 6-7-8 browsers represent 35% of the market (the latest stats <http://www.w3schools.com/browsers/browsers_stats.asp>: IE8, 15%; IE6/7, 20%; Firefox, 47%; Chrome, 12%; Safari, 3.8%) I guess we have to address these -- at least for IE8. Will xhtml compliance bring us up to snuff with IE? > bp > > > Uncaught Exception Encountered java.lang.Error: Unknown search button name 'Study ID' at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:130) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Cookies: JSESSIONID=[319BE70B60E0B5E0E2F817F4A39BD44B] > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-23 03:53:58
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On Mar 22, 2010, at 7:13 PM, Rutger Vos wrote: > I did some checking and fixing to make the static pages all xhtml > compliant. Can we all do that right away when we create html in the > jsps? I know we all pretty much know the rules, but the number of > validation errors in the recently created pages was horrendous :-) > > I fixed the analysis page such that it functions and looks the way > it's supposed to in IE8, but I have no way to check IE7. > > I also added the functionality where all but the last analysis is > collapsed by default. Thanks for the fix. I found a Parallels VM with IE6 on it, so I was able to test that. Then I downloaded IE7 and tested that. IE8 wouldn't install, so I used an emulator (http://www.my-debugbar.com/wiki/IETester/HomePage). Here are the damages: * None of the IE versions can work with our analysis entry forms (the current build -- not yours, obviously) * IE6 and IE7 throw exceptions for almost all of our search buttons (the barf below is from entering a name and clicking the "Author" button -- I guess it's passing 'Study ID' instead of 'authorKeyword' button -- or something like that). * IE8 works on most buttons but fails on the "Discard All Results" buttons (on all tabs) Since IE 6-7-8 browsers represent 35% of the market (the latest stats: IE8, 15%; IE6/7, 20%; Firefox, 47%; Chrome, 12%; Safari, 3.8%) I guess we have to address these -- at least for IE8. Will xhtml compliance bring us up to snuff with IE? bp Uncaught Exception Encountered java.lang.Error: Unknown search button name 'Study ID' at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:130) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Cookies: JSESSIONID=[319BE70B60E0B5E0E2F817F4A39BD44B] |
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From: Rutger V. <rut...@gm...> - 2010-03-22 23:13:39
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I did some checking and fixing to make the static pages all xhtml compliant. Can we all do that right away when we create html in the jsps? I know we all pretty much know the rules, but the number of validation errors in the recently created pages was horrendous :-) I fixed the analysis page such that it functions and looks the way it's supposed to in IE8, but I have no way to check IE7. I also added the functionality where all but the last analysis is collapsed by default. On Mon, Mar 22, 2010 at 8:39 PM, William Piel <wil...@ya...> wrote: > > On Mar 22, 2010, at 4:27 PM, Rutger Vos wrote: > > Is that fair? > > Agreed. In the event that getting IE8 to work does not fix IE7, we can put a > "sorry, go away" message on our web pages (e.g. using javascript to screen > out IE7 browsers). > bp > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-22 21:11:12
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We just got a submission where the submitter had used some fairly unscientific names (e.g. "Bird" "Fish" etc) -- but then used our Taxon Intel feature to map to names that might actually be useful to search on! So I was just thinking... wow. This actually works! bp Taxon Label Taxon Name NCBI taxid uBIO namebankID Ambystomatidae Ambystomatidae 8294 2476828 Ascaphidae Ascaphidae 30311 31759 Bird Aves 8782 21646 Bombinatoridae Bombinatoridae 30312 31782 Caeciliidae Caeciliidae 8446 2476859 Coelacanth Coelacanthiformes 7894 113892 Crocodile Crocodylidae 8493 582627 Cryptobranchidae Cryptobranchidae 30365 31666 Discoglossidae Discoglossidae 8343 2476892 Fish Actinopterygii 7898 113876 Human Homo sapiens 9606 2481730 Hynobiidae Hynobiidae 30366 31668 Ichthyophiidae Ichthyophiidae 8451 31712 Leiopelmatidae Leiopelmatidae 43506 31764 Lizard Squamata 8509 4781680 Lungfish Lepidosireniformes 7879 113905 Marsupial Metatheria 9263 2484208 Pelobatidae Pelobatidae 8432 31776 Pipidae Pipidae 8352 31778 Plethodontidae Plethodontidae 8332 2476829 Rhinatrematidae 1 Rhinatrema 194407 2476887 Rhinatrematidae 2 Epicrionops 43480 2476886 Rhyacotritonidae Rhyacotritonidae 43567 31671 Scolecomorphidae Scolecomorphidae 30378 31714 Sirenidae Sirenidae 8339 31673 Typhlonectidae Typhlonectidae 8454 582595 |
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From: William P. <wil...@ya...> - 2010-03-22 20:39:36
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On Mar 22, 2010, at 4:27 PM, Rutger Vos wrote: > Is that fair? Agreed. In the event that getting IE8 to work does not fix IE7, we can put a "sorry, go away" message on our web pages (e.g. using javascript to screen out IE7 browsers). bp |
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From: Rutger V. <rut...@gm...> - 2010-03-22 20:27:20
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I am going to attempt to make things work with Internet Explorer 8 - which is the one that came with my VM - but I don't think we should be spending time making IE7 happy as well. At this point it's used less often than either IE8, Chrome or Firefox - and usage is obviously dropping (IE9 is now under development). Is that fair? On Mon, Mar 22, 2010 at 12:38 PM, William Piel <wil...@ya...> wrote: > > We have a report (below) that the analysis entries are not visible > in Internet Explorer 7 (except by copy/pasting to a text file). Could > someone with this browser test our interface? I'm guessing that it can't be > the only place that is incompatible. Meanwhile, I'll create a bug report. > bp > > > > > Begin forwarded message: > > From: Ben Wielstra <wie...@it...> > Date: March 22, 2010 6:48:29 AM EDT > To: William Piel <wil...@ya...> > Subject: RE: TreeBASE Submission S10307 > > Dear mister Piel, > > Sorry for my last email, I see the trees are already included in the file. > Thanks for this. > > I have just updated the last field: the analysis. This seems to be not > running smootly yet because I am not able to see what I have filled in here > (using Internet Explorer 7) unless I copy paste it to a text editor. > > There are now some redundant data matrices uploaded which I am not able to > discard. Is it possible to get rid of these? Also, the taxa list seems to > have trouble with the numbers used to code for taxa in the tree block. > > Compared to the old database (which I never used, I only looked at it) there > is now the advantage that the submission number stays the same right? I can > refer to submission 10307 before changing the submission to the ready state? > > Thanks for your troubles, > Ben > > ________________________________________ > Van: William Piel [wil...@ya...] > Verzonden: zondag 21 maart 2010 20:53 > Aan: Ben Wielstra > Onderwerp: TreeBASE Submission S10307 > > Dear Ben Wielstra, > > Thanks for trying out our new version of TreeBASE. > > I noticed that the trees were having trouble getting parsed. In one instance > it was because the "tree" command was missing in the TREES block. In other > instances, a TAXON block was missing, which is a problem for Mesquite v. 2. > > I've uploaded a new version after saving the file in Mesquite. > > (attached is the file I uploaded, in case you want to examine it) > > regards, > > Bill > Faculty of Geo-Information Science and Earth Observation (ITC) > University of Twente > > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-22 16:23:11
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On Mar 22, 2010, at 12:07 PM, Jon Auman wrote: > FYI... > -J Can we do another rebuild to test Youjun's fix for PhyloWidget? (now it should b compatible with Firefox) thanks, Bill |
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From: William P. <wil...@ya...> - 2010-03-22 16:16:22
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On Mar 22, 2010, at 11:29 AM, Rutger Vos wrote: > I don't understand what he means. Is this a phylowidget issue? Yeah. Youjun just fixed that -- the next build should work. bp |
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From: Jon A. <jon...@ne...> - 2010-03-22 16:07:23
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FYI... -J ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: Rutger V. <rut...@gm...> - 2010-03-22 15:29:25
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> I checked the analyses block in Firefox and there it works and I have added > my MrBayes block. I rechecked in IE and there I can now see more details > than previously, but the section 'analysis details' still does not seem to > work. > > I notice that in Firefox errors present in certain sections of the tool box > are highlighted, whereas this is not the case in IE. These issue do sound like they are caused by incompatibilities between IE and prototype. I can probably fix that. > In Firefox I have been unsuccesful to look at the tree. I don't understand what he means. Is this a phylowidget issue? Rutger -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-22 14:24:07
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An update -- after editing with Firefox, he is able to see some things in IE, but not all. bp Begin forwarded message: > From: Ben Wielstra <wie...@it...> > Date: March 22, 2010 9:24:38 AM EDT > To: William Piel <wil...@ya...> > Subject: RE: TreeBASE Submission S10307 > > Dear Bill, > > I checked the analyses block in Firefox and there it works and I have added my MrBayes block. I rechecked in IE and there I can now see more details than previously, but the section 'analysis details' still does not seem to work. > > I notice that in Firefox errors present in certain sections of the tool box are highlighted, whereas this is not the case in IE. > > In Firefox I have been unsuccesful to look at the tree. > > Thanks, > Ben > |
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From: Rutger V. <rut...@gm...> - 2010-03-22 13:03:52
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I'm downloading vmware right now, I still have an xp vm that I used for coding previously, so I should be able to debug the JavaScript soonish. I know that the prototype js library we're using for dynamic GUI elements needs to be used with a bit more care in ie than other browsers (because Element cannot be extended in the same way). I've tried to be dilligent with it, but I obviously don't always have an extra virtual machine running just to check how Internet Explorer decides to break the rules this time. On Monday, March 22, 2010, William Piel <wil...@ya...> wrote: > > We have a report (below) that the analysis entries are not visible in Internet Explorer 7 (except by copy/pasting to a text file). Could someone with this browser test our interface? I'm guessing that it can't be the only place that is incompatible. Meanwhile, I'll create a bug report. > bp > > > > > Begin forwarded message: > From: Ben Wielstra <wie...@it...> > Date: March 22, 2010 6:48:29 AM EDT > To: William Piel <wil...@ya...> > Subject: RE: TreeBASE Submission S10307 > > Dear mister Piel, > > Sorry for my last email, I see the trees are already included in the file. Thanks for this. > > I have just updated the last field: the analysis. This seems to be not running smootly yet because I am not able to see what I have filled in here (using Internet Explorer 7) unless I copy paste it to a text editor. > > There are now some redundant data matrices uploaded which I am not able to discard. Is it possible to get rid of these? Also, the taxa list seems to have trouble with the numbers used to code for taxa in the tree block. > > Compared to the old database (which I never used, I only looked at it) there is now the advantage that the submission number stays the same right? I can refer to submission 10307 before changing the submission to the ready state? > > Thanks for your troubles, > Ben > > ________________________________________ > Van: William Piel [wil...@ya...] > Verzonden: zondag 21 maart 2010 20:53 > Aan: Ben Wielstra > Onderwerp: TreeBASE Submission S10307 > > Dear Ben Wielstra, > > Thanks for trying out our new version of TreeBASE. > > I noticed that the trees were having trouble getting parsed. In one instance it was because the "tree" command was missing in the TREES block. In other instances, a TAXON block was missing, which is a problem for Mesquite v. 2. > > I've uploaded a new version after saving the file in Mesquite. > > (attached is the file I uploaded, in case you want to examine it) > > regards, > > Bill > Faculty of Geo-Information Science and Earth Observation (ITC) > University of Twente > > > > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-22 12:38:40
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We have a report (below) that the analysis entries are not visible in Internet Explorer 7 (except by copy/pasting to a text file). Could someone with this browser test our interface? I'm guessing that it can't be the only place that is incompatible. Meanwhile, I'll create a bug report. bp Begin forwarded message: > From: Ben Wielstra <wie...@it...> > Date: March 22, 2010 6:48:29 AM EDT > To: William Piel <wil...@ya...> > Subject: RE: TreeBASE Submission S10307 > > Dear mister Piel, > > Sorry for my last email, I see the trees are already included in the file. Thanks for this. > > I have just updated the last field: the analysis. This seems to be not running smootly yet because I am not able to see what I have filled in here (using Internet Explorer 7) unless I copy paste it to a text editor. > > There are now some redundant data matrices uploaded which I am not able to discard. Is it possible to get rid of these? Also, the taxa list seems to have trouble with the numbers used to code for taxa in the tree block. > > Compared to the old database (which I never used, I only looked at it) there is now the advantage that the submission number stays the same right? I can refer to submission 10307 before changing the submission to the ready state? > > Thanks for your troubles, > Ben > > ________________________________________ > Van: William Piel [wil...@ya...] > Verzonden: zondag 21 maart 2010 20:53 > Aan: Ben Wielstra > Onderwerp: TreeBASE Submission S10307 > > Dear Ben Wielstra, > > Thanks for trying out our new version of TreeBASE. > > I noticed that the trees were having trouble getting parsed. In one instance it was because the "tree" command was missing in the TREES block. In other instances, a TAXON block was missing, which is a problem for Mesquite v. 2. > > I've uploaded a new version after saving the file in Mesquite. > > (attached is the file I uploaded, in case you want to examine it) > > regards, > > Bill > Faculty of Geo-Information Science and Earth Observation (ITC) > University of Twente > > |
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From: Rutger V. <rut...@gm...> - 2010-03-22 10:39:13
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> ps - Frankly, I was hoping that the whole idea of using Mesquite was that it > would be a gatekeeper for preventing trash from getting in -- apparently > not. Yeah, this is unfortunate - but not even Mesquite can actually "validate" nexus files, it just gives it its best shot. Which is why NeXML is so great, of course. |
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From: Jon A. <jon...@ne...> - 2010-03-22 02:02:56
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I think they are respecting robots.txt now. The database volume has not grown for hours and the apache logs no longer show google searching the database. -Jon On Mar 21, 2010, at 9:05 PM, William Piel wrote: > > On Mar 21, 2010, at 5:30 PM, Jon Auman wrote: > >> Yes, the file system is running out of space. And google wasn't honoring the robots.txt. Since the last reboot, it seems that no spiders are searching the site, so let's see how that goes. >> >> It wasn't just google, but msn, snap.com, baidu.com, ro...@ga... (WTF?), etc. It was like hey boys, I found a 100GB database, let's index it! >> >> Anywho, I'll be keeping an eye on it. No temp files for the last 1/2 hour. >> >> -Jon > > Wow. Thanks Jon. Indeed, in TreebASE1, I found plenty of robots did not respect robots.txt -- when they hit, it would slow me down and I'd listen to a lot of disk activity noise all day... > > But I can't help but think -- if we can't keep TreeBASE up for more than a few hours at a time, might it make more sense to pause on the press release until have a lasting solution? I'm concerned that when we make an announcement and all sorts of people head to the site to check it out, I don't want their first experience to be one of an exception barf. > > bp > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: William P. <wil...@ya...> - 2010-03-22 01:05:28
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On Mar 21, 2010, at 5:30 PM, Jon Auman wrote: > Yes, the file system is running out of space. And google wasn't honoring the robots.txt. Since the last reboot, it seems that no spiders are searching the site, so let's see how that goes. > > It wasn't just google, but msn, snap.com, baidu.com, ro...@ga... (WTF?), etc. It was like hey boys, I found a 100GB database, let's index it! > > Anywho, I'll be keeping an eye on it. No temp files for the last 1/2 hour. > > -Jon Wow. Thanks Jon. Indeed, in TreebASE1, I found plenty of robots did not respect robots.txt -- when they hit, it would slow me down and I'd listen to a lot of disk activity noise all day... But I can't help but think -- if we can't keep TreeBASE up for more than a few hours at a time, might it make more sense to pause on the press release until have a lasting solution? I'm concerned that when we make an announcement and all sorts of people head to the site to check it out, I don't want their first experience to be one of an exception barf. bp |
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From: William P. <wil...@ya...> - 2010-03-22 00:59:39
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We had our first attempt to submit data. A Dutchman, Ben Wielstra, has been uploading NEXUS files -- some a bit malformed (as is common). However, because issue 2960886 has not been fixed, we can't get rid of the junk data. Plus, even if we could delete a matrix (or tree), taxon labels that are exclusively linked to that matrix will not be deleted with them. So, as we resolve 2960886 I think it's important to also simultaneously delete any taxon labels linked to the deleted object but not found in any other tree or matrix. As bad data gets in, the taxon label table gets crowded with a lot of garbage. Attached, you can see that his "Taxon Labels Information" page is loaded with weird things like numbers and semi-colons -- things that crept in via poorly NEXUS in which Mesquite did a botched job of parsing. (also it's got the repeated names, per issue 2973661). bp ps - Frankly, I was hoping that the whole idea of using Mesquite was that it would be a gatekeeper for preventing trash from getting in -- apparently not. |
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From: Jon A. <jon...@ne...> - 2010-03-21 21:30:12
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Yes, the file system is running out of space. And google wasn't honoring the robots.txt. Since the last reboot, it seems that no spiders are searching the site, so let's see how that goes. It wasn't just google, but msn, snap.com, baidu.com, ro...@ga... (WTF?), etc. It was like hey boys, I found a 100GB database, let's index it! Anywho, I'll be keeping an eye on it. No temp files for the last 1/2 hour. -Jon On Mar 21, 2010, at 5:18 PM, Vladimir Gapeyev wrote: > > On Mar 21, 2010, at 4:29 PM, William Piel wrote: > >> Caused by: org.postgresql.util.PSQLException: ERROR: could not seek >> to end of segment 0 of relation base/73916/74290: Read-only file >> system > > > Jon, > The above looks like the core exception in both of Bill's recent > reports. Could it be that, besides being read-only, the file system > runs out of space or the relation is corrupted? These are only > guesses, though. > --VG > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: Vladimir G. <vla...@du...> - 2010-03-21 21:18:19
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On Mar 21, 2010, at 4:29 PM, William Piel wrote: > Caused by: org.postgresql.util.PSQLException: ERROR: could not seek > to end of segment 0 of relation base/73916/74290: Read-only file > system Jon, The above looks like the core exception in both of Bill's recent reports. Could it be that, besides being read-only, the file system runs out of space or the relation is corrupted? These are only guesses, though. --VG |
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From: William P. <wil...@ya...> - 2010-03-21 20:30:00
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On Mar 21, 2010, at 3:38 PM, Jon Auman wrote: > I've restarted the server. I've also added a robots.txt file to block *all* robots. It was up for some time, but now when I do a search I get an exception. bp Uncaught Exception Encountered org.hibernate.exception.SQLGrammarException: could not execute query at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.doList(Loader.java:2216) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104) at org.hibernate.loader.Loader.list(Loader.java:2099) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569) at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283) at org.hibernate.impl.CriteriaImpl$Subcriteria.list(CriteriaImpl.java:458) at org.cipres.treebase.dao.study.StudyDAO.findByAuthor(StudyDAO.java:224) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy63.findByAuthor(Unknown Source) at org.cipres.treebase.service.study.StudyServiceImpl.findByAuthor(StudyServiceImpl.java:423) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.findByAuthor(Unknown Source) at org.cipres.treebase.web.controllers.StudySearchController.doSearch(StudySearchController.java:277) at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:132) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Caused by: org.postgresql.util.PSQLException: ERROR: could not seek to end of segment 0 of relation base/73916/74290: Read-only file system at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1592) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1327) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:192) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:451) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:350) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:254) at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:93) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186) at org.hibernate.loader.Loader.getResultSet(Loader.java:1787) at org.hibernate.loader.Loader.doQuery(Loader.java:674) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236) at org.hibernate.loader.Loader.doList(Loader.java:2213) ... 84 more Cookies: JSESSIONID=[5B4317D7894DB80066B13D0ED75F6270] __utma=[216002130.839762607.1263756393.1264687215.1264739521.8] __utmz=[216002130.1263756393.1.1.utmccn] |
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